[gmx-developers] Clusterizing a long-time trajectories

[Boris Timofeev]

Dear David!
thank you for your letter,
could you give me some references  of incremental clustering  algorithm  to start with?
Thank you in advance,
sincerely yours, 
Boris Timofeev


>Воскресенье,  5 августа 2018, 23:46 +03:00 от David van der Spoel <spoel at xray.bmc.uu.se>:
>
>Den 2018-08-04 kl. 23:00, skrev Boris Timofeev:
>> Dear David!
>> 
>> Option  -dr, it is new?
>> Perhaps, you meant - dt? There is no wish to thin out a trajectory.
>-dt indeed. The reason for long simulations is typically that 
>transitions are slow and that it take long time to equilibrate. That 
>also means that frames near each other are highly correlated and 
>therefore the -dt option is no problem. However, this is obviously 
>problem dependent.
>
>It could be possible to devise some kind of incremental clustering 
>algorithm that stores cluster centers and dynamically updates them. In 
>that manner the whole trajectory does not need to be stored. However 
>that would be a research project in itself, and I guess this kind of 
>algorithms has been developed long time ago. If you find such an 
>algorithm you could consider implementing it. Alternatively, if you see 
>a way of getting around the N^2 RMSD matrix in the existing algorithms 
>that would be interesting too.
>
>> Sincerely,
>> Boris.
>> 
>> 
>>     Суббота, 4 августа 2018, 16:09 +03:00 от David van der Spoel
>>     < spoel at xray.bmc.uu.se >:
>> 
>>     Den 2018-07-26 kl. 14:02, skrev Boris Timofeev:
>>      > Dear developers!
>>      >
>>      > The existing realization of "gmx cluster" for calculations uses
>>      > RMSD-matrix,
>>      > quadratically increasing with increase in length of a trajectory,
>>      > and already since 20000 frames calculation of clusters becomes
>>     impossible
>>      > because of requirements to memory and time.
>>      >
>>      > Whether there are some special methods for a clustering of
>>     trajectories
>>      > of big duration,
>>      > containing 100000 and more frames?
>>     Use the -dr flag.
>>      >
>>      > Best wishes
>>      > Boris Timofeev.
>>      >
>>      >
>>      >
>>      >
>>      >
>> 
>> 
>>     -- 
>>     David van der Spoel, Ph.D., Professor of Biology
>>     Head of Department, Cell & Molecular Biology, Uppsala University.
>>     Box 596, SE-75124 Uppsala, Sweden. Phone:  +46184714205 .
>>  http://www.icm.uu.se
>>     -- 
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>> 
>> 
>> -- 
>> Boris Timofeev
>> 
>> 
>
>
>-- 
>David van der Spoel, Ph.D., Professor of Biology
>Head of Department, Cell & Molecular Biology, Uppsala University.
>Box 596, SE-75124 Uppsala, Sweden. Phone:  +46184714205 .
>http://www.icm.uu.se
>-- 
>Gromacs Developers mailing list
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-- 
Boris Timofeev
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